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Crystal structure of CLK3 in complex with macrocycle ODS2004070
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277.15 18% PEG 3350, 0.2M potassium/sodium phosphate, 0.1M bis-tris-propane pH 7.0, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.99 58.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.73 α = 90 b = 131.36 β = 107.8 c = 83.8 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2012-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 79.788 95.5 0.073 0.083 0.038 10.7 4.5 104048 104048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 96.5 0.733 0.733 0.83 0.382 1 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2eu9 1.7 37.99 98842 5204 95.37 0.1584 0.1565 0.1697 0.195 0.2043 RANDOM 26.552
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.32 -0.84 -0.53 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.681 r_dihedral_angle_4_deg 21.542 r_dihedral_angle_3_deg 13.503 r_dihedral_angle_1_deg 6.331 r_angle_refined_deg 1.807 r_angle_other_deg 1.441 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.681 r_dihedral_angle_4_deg 21.542 r_dihedral_angle_3_deg 13.503 r_dihedral_angle_1_deg 6.331 r_angle_refined_deg 1.807 r_angle_other_deg 1.441 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5885 Nucleic Acid Atoms Solvent Atoms 929 Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing